''We know there are contaminants in the sediments in some estuaries in NSW but we didn't know what impact they were having on the marine life living in the water until now,'' research supervisor Emma Johnston said.

The study of 10 NSW estuaries, the first of its kind to measure the effect of toxins on marine animals rather than just measure the level of contaminants in the water or sediment, suggests the pollutants might also be harming other species.

''There are hot spots of contamination throughout estuaries in NSW and we need to find ways to ameliorate that problem because it is causing ongoing ecological damage,'' Professor Johnston said.

Although oysters were a hardy species and could survive in heavily polluted areas, they accumulated contaminants such as metals in their tissues, which made them an ideal ''bio-monitor'' to assess the overall health of a waterway, she said.

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As part of the study, marine ecotoxicologist Katelyn Edge deployed bags of oysters at 58 sites in 10 estuaries along the coast.

After three months Dr Edge, who conducted the research as part of her PhD, measured the level of contaminants in the sediment on the estuary floor, in the water column and in the tissue of the oysters.

''Where the concentration of contaminant was high in both the sediment and oysters' tissue we found really high stress levels in the oysters,'' said Dr Edge, who published her findings in the journal Chemosphere.

The most heavily contaminated estuaries were Port Jackson, Port Kembla, Botany Bay and the Hunter River in Newcastle, she said.

The Clyde, Port Hacking, Broken Bay, Karuah River and the Wagonga Inlet were the cleanest waterways.

Professor Johnston said the findings were a counter to arguments against remediating contaminated sites because their results showed metals in the sediments were causing problems for animals living above the estuary floor.

'''Just leave it there, it'll be fine' is an argument we have heard.''

In waterways such as Sydney Harbour, ferries and boats were constantly stirring sediments and dragging contaminants into the water column, she said.

''There are some locations in Sydney Harbour that are some of the most contaminated in the world and rarely is anything done about it,'' Professor Johnston said.

In laboratory studies Dr Edge found high levels of metals inside the oysters' tissues would rupture structures inside their cells, affecting the ability to reproduce.

Sydney rock oysters, a native species found along the coast from Queensland to Tasmania and South Australia, should be used as a biomarker during future developments or dredging to assess the impact on marine ecosystems.